123 lines
3.8 KiB
Groff
123 lines
3.8 KiB
Groff
LAMMPS (18 Feb 2013)
|
|
# Rhodopsin model
|
|
|
|
newton off
|
|
package gpu force/neigh 0 1 1
|
|
|
|
variable x index 2
|
|
variable y index 2
|
|
variable z index 2
|
|
|
|
units real
|
|
neigh_modify delay 5 every 1
|
|
|
|
atom_style full
|
|
bond_style harmonic
|
|
angle_style charmm
|
|
dihedral_style charmm
|
|
improper_style harmonic
|
|
pair_style lj/charmm/coul/long/gpu 8.0 10.0
|
|
pair_modify mix arithmetic
|
|
kspace_style pppm/gpu 1e-4
|
|
|
|
read_data data.rhodo
|
|
4 = max bonds/atom
|
|
18 = max angles/atom
|
|
40 = max dihedrals/atom
|
|
4 = max impropers/atom
|
|
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
|
1 by 2 by 2 MPI processor grid
|
|
32000 atoms
|
|
32000 velocities
|
|
27723 bonds
|
|
40467 angles
|
|
56829 dihedrals
|
|
1034 impropers
|
|
4 = max # of 1-2 neighbors
|
|
12 = max # of 1-3 neighbors
|
|
24 = max # of 1-4 neighbors
|
|
26 = max # of special neighbors
|
|
|
|
replicate $x $y $z
|
|
replicate 2 $y $z
|
|
replicate 2 2 $z
|
|
replicate 2 2 2
|
|
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
|
1 by 2 by 2 MPI processor grid
|
|
256000 atoms
|
|
221784 bonds
|
|
323736 angles
|
|
454632 dihedrals
|
|
8272 impropers
|
|
4 = max # of 1-2 neighbors
|
|
12 = max # of 1-3 neighbors
|
|
24 = max # of 1-4 neighbors
|
|
26 = max # of special neighbors
|
|
|
|
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
|
12936 = # of size 2 clusters
|
|
29064 = # of size 3 clusters
|
|
5976 = # of size 4 clusters
|
|
33864 = # of frozen angles
|
|
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
|
|
|
special_bonds charmm
|
|
|
|
thermo 100
|
|
thermo_style multi
|
|
timestep 2.0
|
|
|
|
run 200
|
|
PPPM initialization ...
|
|
G vector (1/distance) = 0.245959
|
|
grid = 48 64 60
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0410392
|
|
estimated relative force accuracy = 0.000123588
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 68635 46080
|
|
Memory usage per processor = 250.358 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = 157024.0492 KinEng = 172792.6155 Temp = 301.1796
|
|
PotEng = -15768.5663 E_bond = 28164.9917 E_angle = 117224.0742
|
|
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
|
|
E_coul = 1894295.6622 E_long = -2130488.8032 Press = 9562.1554
|
|
Volume = 2457390.7959
|
|
---------------- Step 100 ----- CPU = 12.1280 (sec) ----------------
|
|
TotEng = -233301.6590 KinEng = 123222.8183 Temp = 214.7789
|
|
PotEng = -356524.4772 E_bond = 13098.4683 E_angle = 56766.9228
|
|
E_dihed = 45556.8211 E_impro = 1313.9369 E_vdwl = -40863.9000
|
|
E_coul = 1705084.8591 E_long = -2137481.5855 Press = -1634.3808
|
|
Volume = 2522232.6313
|
|
---------------- Step 200 ----- CPU = 23.3169 (sec) ----------------
|
|
TotEng = -308342.2597 KinEng = 108936.8553 Temp = 189.8783
|
|
PotEng = -417279.1150 E_bond = 9579.0042 E_angle = 47373.6037
|
|
E_dihed = 39847.3737 E_impro = 967.6451 E_vdwl = -23631.6382
|
|
E_coul = 1646630.1738 E_long = -2138045.2773 Press = -1185.5491
|
|
Volume = 2554682.9808
|
|
Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms
|
|
|
|
Pair time (%) = 4.29395 (18.4156)
|
|
Bond time (%) = 6.57406 (28.1944)
|
|
Kspce time (%) = 4.75311 (20.3848)
|
|
Neigh time (%) = 1.32057 (5.66359)
|
|
Comm time (%) = 0.555436 (2.38212)
|
|
Outpt time (%) = 0.000431776 (0.00185177)
|
|
Other time (%) = 5.81936 (24.9577)
|
|
|
|
FFT time (% of Kspce) = 1.78333 (37.5192)
|
|
FFT Gflps 3d (1d only) = 5.0126 11.639
|
|
|
|
Nlocal: 64000 ave 64003 max 63997 min
|
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
Nghost: 70636.8 ave 70640 max 70632 min
|
|
Histogram: 1 0 0 0 0 0 1 1 0 1
|
|
Neighs: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 0
|
|
Ave neighs/atom = 0
|
|
Ave special neighs/atom = 7.43187
|
|
Neighbor list builds = 31
|
|
Dangerous builds = 12
|